Documentation can be found here: https://outbreak-local-documentation.readthedocs.io/en/latest/
Outbreak.info local build is a spin-off project of outbreak.info from Scripps Research that encourages users to launch their own genomic analysis platforms using custom data sets. It allows users to take their own sequencing data and metadata, and build an individual database, server, and website with similar functionality to the "Variants" arm of outbreak.info with only a configuration file and several terminal commands.
- Sequencing data is preprocessed with Bjorn.
- Data in ingested into an ElasticSearch index.
- ElasticSearch, Tornado, and the client side all launch in individual docker containers for a customized build.
During outbreaks of emerging diseases such as COVID-19, efficiently collecting, sharing, and integrating data is critical to scientific research.
outbreak.info is a standardized, searchable platform to discover and explore COVID-19 and SARS-CoV-2 data from the Center for Viral Systems Biology at Scripps Research. It contains three parts: a standardized searchable database of COVID-19 research; customizable real-time surveillance reports on SARS-CoV-2 variants and mutations; and an explorable interface to examine changes in epidemiological data.
Disclaimer: This project is a work-in progress. Please submit an issue if you notice any bugs or want to suggest features.